Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles
G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world’s most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and ...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Cagirici, H. B., Sen, T. Z. Tags: Investigations Source Type: research
Genome-Wide Changes in Genetic Diversity in a Population of Myotis lucifugus Affected by White-Nose Syndrome
Novel pathogens can cause massive declines in populations, and even extirpation of hosts. But disease can also act as a selective pressure on survivors, driving the evolution of resistance or tolerance. Bat white-nose syndrome (WNS) is a rapidly spreading wildlife disease in North America. The fungus causing the disease invades skin tissues of hibernating bats, resulting in disruption of hibernation behavior, premature energy depletion, and subsequent death. We used whole-genome sequencing to investigate changes in allele frequencies within a population of Myotis lucifugus in eastern North America to search for genetic res...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Lilley, T. M., Wilson, I. W., Field, K. A., Reeder, D. M., Vodzak, M. E., Turner, G. G., Kurta, A., Blomberg, A. S., Hoff, S., Herzog, C. J., Sewall, B. J., Paterson, S. Tags: Investigations Source Type: research
Genomic Structure, Evolutionary Origins, and Reproductive Function of a Large Amplified Intrinsically Disordered Protein-Coding Gene on the X Chromosome (Laidx) in Mice
Mouse sex chromosomes are enriched for co-amplified gene families, present in tens to hundreds of copies. Co-amplification of Slx/Slxl1 on the X chromosome and Sly on the Y chromosome are involved in dose-dependent meiotic drive, however the role of other co-amplified genes remains poorly understood. Here we demonstrate that the co-amplified gene family on the X chromosome, Srsx, along with two additional partial gene annotations, is actually part of a larger transcription unit, which we name Laidx. Laidx is harbored in a 229 kb amplicon that represents the ancestral state as compared to a 525 kb Y-amplicon containing the ...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Arlt, M. F., Brogley, M. A., Stark-Dykema, E. R., Hu, Y.-C., Mueller, J. L. Tags: Genetics of Sex Source Type: research
A Collection of Pre-mRNA Splicing Mutants in Arabidopsis thaliana
To investigate factors influencing pre-mRNA splicing in plants, we conducted a forward genetic screen using an alternatively-spliced GFP reporter gene in Arabidopsis thaliana. This effort generated a collection of sixteen mutants impaired in various splicing-related proteins, many of which had not been recovered in any prior genetic screen or implicated in splicing in plants. The factors are predicted to act at different steps of the spliceosomal cycle, snRNP biogenesis pathway, transcription, and mRNA transport. We have described eleven of the mutants in recent publications. Here we present the final five mutants, which a...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Kanno, T., Venhuizen, P., Wu, M.-T., Chiou, P., Chang, C.-L., Kalyna, M., Matzke, A. J. M., Matzke, M. Tags: Investigations Source Type: research
Forebrain Transcriptional Response to Transient Changes in Circulating Androgens in a Cichlid Fish
It has been hypothesized that androgens respond to the social interactions as a way to adjust the behavior of individuals to the challenges of the social environment in an adaptive manner. Therefore, it is expected that transient changes in circulating androgen levels within physiological scope should impact the state of the brain network that regulates social behavior, which should translate into adaptive behavioral changes. Here, we examined the effect that a transient peak in androgen circulating levels, which mimics socially driven changes in androgen levels, has on the forebrain state, which harbors most nuclei of the...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Felix, A. S., Cardoso, S. D., Roleira, A., Oliveira, R. F. Tags: Investigations Source Type: research
Genetic and Physiological Characterization of a Calcium Deficiency Phenotype in Maize
Calcium (Ca) is an essential plant nutrient, required for signaling, cell wall fortification and growth and development. Calcium deficiency (Ca-deficiency) in maize causes leaf tip rot and a so-called "bull-whipping" or "buggy-whipping" phenotype. Seedlings of the maize line B73 displayed these Ca-deficiency-like symptoms when grown in the greenhouse with excess fertilizer during the winter months, while seedlings of the Mo17 maize line did not display these symptoms under the same conditions. These differential phenotypes could be recapitulated in ‘mini-hydroponic’ systems in the laboratory in which high ammon...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Wang, Y., Martins, L. B., Sermons, S., Balint-Kurti, P. Tags: Investigations Source Type: research
ngn-1/neurogenin Activates Transcription of Multiple Terminal Selector Transcription Factors in the Caenorhabditis elegans Nervous System
The objective of this study was to further elucidate the role of ngn-1/neurogenin in nervous system development and to identify its downstream transcriptional targets, using the nematode Caenorhabditis elegans as a model for this work. We found that ngn-1 is required for axon outgrowth, nerve ring architecture, and neuronal cell fate specification. We also showed that ngn-1 may have roles in neuroblast migration and epithelial integrity during embryonic development. Using RNA sequencing and comparative transcriptome analysis, we identified eight transcription factors (hlh-34/NPAS1, unc-42/PROP1, ceh-17/PHOX2A, lim-4/LHX6, ...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Christensen, E. L., Beasley, A., Radchuk, J., Mielko, Z. E., Preston, E., Stuckett, S., Murray, J. I., Hudson, M. L. Tags: Investigations Source Type: research
Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout
Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Smith, S. R., Amish, S. J., Bernatchez, L., Le Luyer, J., C. Wilson, C., Boeberitz, O., Luikart, G., Scribner, K. T. Tags: Investigations Source Type: research
An NCBP3-Domain Protein Mediates Meiotic Silencing by Unpaired DNA
We report here that SAD-8, a protein similar to human NCBP3, also mediates silencing. Although SAD-8 is not essential for either vegetative or sexual development, it is required for MSUD. SAD-8 localizes predominantly in the nucleus and interacts with both NCBP1 and NCBP2. Similar to NCBP1 and NCBP2, SAD-8 interacts with a component (Argonaute) of the perinuclear meiotic silencing complex (MSC), further implicating the involvement of cap-binding proteins in silencing. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Boone, E. C., Xiao, H., Vierling, M. M., Decker, L. M., Sy, V. T., Kennedy, R. F., Bonham, M. A., Schmitz, S. F., John, A. M., Hammond, T. M., Shiu, P. K. T. Tags: Investigations Source Type: research
MoBPS - Modular Breeding Program Simulator
The R-package MoBPS provides a computationally efficient and flexible framework to simulate complex breeding programs and compare their economic and genetic impact. Simulations are performed on the base of individuals. MoBPS utilizes a highly efficient implementation with bit-wise data storage and matrix multiplications from the associated R-package miraculix allowing to handle large scale populations. Individual haplotypes are not stored but instead automatically derived based on points of recombination and mutations. The modular structure of MoBPS allows to combine rather coarse simulations, as needed to generate founder...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Pook, T., Schlather, M., Simianer, H. Tags: Software and Data Resources Source Type: research
In Vivo Visual Screen for Dopaminergic Rab {leftrightarrow} LRRK2-G2019S Interactions in Drosophila Discriminates Rab10 from Rab3
LRRK2 mutations cause Parkinson’s, but the molecular link from increased kinase activity to pathological neurodegeneration remains undetermined. Previous in vitro assays indicate that LRRK2 substrates include at least 8 Rab GTPases. We have now examined this hypothesis in vivo in a functional, electroretinogram screen, expressing each Rab with/without LRRK2-G2019S in selected Drosophila dopaminergic neurons. Our screen discriminated Rab10 from Rab3. The strongest Rab/LRRK2-G2019S interaction is with Rab10; the weakest with Rab3. Rab10 is expressed in a different set of dopaminergic neurons from Rab3. Thus, anatomical...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Petridi, S., Middleton, C. A., Ugbode, C., Fellgett, A., Covill, L., Elliott, C. J. H. Tags: Mutant Screen Report Source Type: research
A Method for Rapid Selection of Randomly Induced Mutations in a Gene of Interest Using CRISPR/Cas9 Mediated Activation of Gene Expression
We have developed a CRISPR/Cas9 based method for isolating randomly induced recessive lethal mutations in a gene of interest (GOI) by selection within the F1 progeny of a single genetic cross. Our method takes advantage of the ability to overexpress a GOI using CRISPR/Cas9 mediated activation of gene expression. In essence, the screening strategy is based upon the idea that if overexpression of a wild type allele can generate a phenotype, then overexpression of a newly induced loss-of-function allele will lack this phenotype. As a proof-of-principle, we used this method to select EMS induced mutations of the Drosophila gen...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Ng, W. A., Ma, A., Chen, M., Reed, B. H. Tags: Mutant Screen Report Source Type: research
Genetic Selection Based on a Ste6*C-HA-Ura3 Substrate Identifies New Cytosolic Quality Control Alleles in Saccharomyces cerevisiae
In this study, we developed a CytoQC reporter substrate, Ste6*C-HA-Ura3, for a new genetic selection of spontaneous CytoQC mutations in the yeast Saccharomyces cerevisiae. In addition to UBR1, which encodes for a known CytoQC E3 ligase, we identified six new CytoQC candidates. In the preliminary characterization of two mutants, we found that Doa4 is involved in the degradation of misfolded substrates while Pup2 functions in the selectivity of CytoQC and ERAD substrates. Overall, the strategy demonstrates the potential to identify novel genes and advance our understanding of CytoQC. (Source: G3: Genes Genomes Genetics)
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Chan, S. N., Prasad, R., Matsudaira, P. Tags: Mutant Screen Report Source Type: research
A Genome-Wide Screen in Mice To Identify Cell-Extrinsic Regulators of Pulmonary Metastatic Colonisation
Metastatic colonization, whereby a disseminated tumor cell is able to survive and proliferate at a secondary site, involves both tumor cell-intrinsic and -extrinsic factors. To identify tumor cell-extrinsic (microenvironmental) factors that regulate the ability of metastatic tumor cells to effectively colonize a tissue, we performed a genome-wide screen utilizing the experimental metastasis assay on mutant mice. Mutant and wildtype (control) mice were tail vein-dosed with murine metastatic melanoma B16-F10 cells and 10 days later the number of pulmonary metastatic colonies were counted. Of the 1,300 genes/genetic locations...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: van der Weyden, L., Swiatkowska, A., Iyer, V., Speak, A. O., Adams, D. J. Tags: Mutant Screen Report Source Type: research
A Genome-Wide Screen for Genes Affecting Spontaneous Direct-Repeat Recombination in Saccharomyces cerevisiae
Homologous recombination is an important mechanism for genome integrity maintenance, and several homologous recombination genes are mutated in various cancers and cancer-prone syndromes. However, since in some cases homologous recombination can lead to mutagenic outcomes, this pathway must be tightly regulated, and mitotic hyper-recombination is a hallmark of genomic instability. We performed two screens in Saccharomyces cerevisiae for genes that, when deleted, cause hyper-recombination between direct repeats. One was performed with the classical patch and replica-plating method. The other was performed with a high-through...
Source: G3: Genes Genomes Genetics - May 31, 2020 Category: Genetics & Stem Cells Authors: Novarina, D., Desai, R., Vaisica, J. A., Ou, J., Bellaoui, M., Brown, G. W., Chang, M. Tags: Mutant Screen Report Source Type: research
